The music situation is always really fluid, it's not uncommon to have a particular song in the film but a different song on the DVDs and VOD for rights reasons. Also it's not unheard of for the studio to replace a song after the film's released, they used to ship new reels to the theater but now they just upload a new DCP to the theatre chain headquarters, they all program it from their via satellite.
It's the music supervisor's job to clear all the music, he'll give the picture editor music that he thinks he can clear and then he'll start negotiation if it takes. By the time the final mix is happening he'll usually at least have all the music in negotiation and there won't be any music that's flat off-limits. It sounds like here he started to clear the song and he probably had the number in his spreadsheet (I'm not up on my rates but a $50k-$100k buyout for this usage in all media would kinda be standard). They just didn't do the paperwork -- add to this the artist might have gotten cold feet after the hack when it was alleged that North Korea was involved.
They might update the mix with a different song and just settle with the label. This is what Errors & Omissions insurance is for.